RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10887
(222 letters)
>gnl|CDD|214683 smart00477, NUC, DNA/RNA non-specific endonuclease. prokaryotic
and eukaryotic double- and single-stranded DNA and RNA
endonucleases also present in phosphodiesterases.
Length = 210
Score = 199 bits (508), Expect = 7e-65
Identities = 88/192 (45%), Positives = 111/192 (57%), Gaps = 5/192 (2%)
Query: 16 DFVLSYDRRNRTAYWVFEHLTKENTAYSEAVNRSKSEFFEDDSIHEYFRGRNSDYKYSGY 75
+VL Y+R R WV H+T E R F D I E F+ + SDYK SGY
Sbjct: 3 QYVLGYNRSTRMPNWVAYHITGELLT--SGAERKSDCFKPDTRIPEKFQAKLSDYKGSGY 60
Query: 76 DRGHLAAAGNHKANQKHLDQTFVLSNISPQVGAGFNRDKWAELEKHSRKLL-KQYPNVYV 134
DRGHLA A +HK + + + TF LSNI PQ FNR WA LE + RKL + VYV
Sbjct: 61 DRGHLAPAADHKFSSEAMADTFYLSNIVPQYP-DFNRGAWAYLEDYLRKLTASERNGVYV 119
Query: 135 CTGPLYLPMKSPNGKK-YVNYEVIGDSNVAVPTHFFKIIVAENENGKLVMENYVLPNAVI 193
+GPL+LP G K V Y+VIG NVA+PTHFFK+I AE + L + ++LPN I
Sbjct: 120 VSGPLFLPNYDGKGDKLEVKYQVIGSKNVAIPTHFFKVITAEKADSYLEVAAFILPNDPI 179
Query: 194 SDSTPLTSFMVS 205
+D +PLT+F V
Sbjct: 180 NDESPLTNFRVP 191
>gnl|CDD|238043 cd00091, NUC, DNA/RNA non-specific endonuclease; prokaryotic and
eukaryotic double- and single-stranded DNA and RNA
endonucleases also present in phosphodiesterases. They
exists as monomers and homodimers.
Length = 241
Score = 192 bits (491), Expect = 7e-62
Identities = 84/203 (41%), Positives = 119/203 (58%), Gaps = 8/203 (3%)
Query: 1 MKYGFPSLDS---LRSFDDFVLSYDRRNRTAYWVFEHLTKENTAYSEAVNRSKSEFFEDD 57
++YG P + + + S+ +VLSY+R R WV EH+ KE+ + V+R +F +D
Sbjct: 1 LQYGRPGVLADTEVLSYTHYVLSYNRATRLPLWVAEHIDKED--LGKNVDRKYDQFKQDP 58
Query: 58 SIHEYFRGRNSDYKYSG-YDRGHLAAAGNHKANQKHLDQTFVLSNISPQVGAGFNRDKWA 116
I F NSDYK SG DRGHLA A + +Q D TF L+N++PQV GFN+ WA
Sbjct: 59 RIPPLFSATNSDYKGSGSLDRGHLAPAADPVWSQDAQDATFYLTNMAPQVQ-GFNQGNWA 117
Query: 117 ELEKHSRKL-LKQYPNVYVCTGPLYLPMKSPNGKKYVNYEVIGDSNVAVPTHFFKIIVAE 175
LE + R L + +VYV TGPL+LP +G Y++ +VI + VAVPTHF+K+I+ E
Sbjct: 118 YLEDYLRDLAASEGKDVYVVTGPLFLPDLDGDGGSYLSTQVINNGKVAVPTHFWKVIIDE 177
Query: 176 NENGKLVMENYVLPNAVISDSTP 198
G L + +VLPN D+
Sbjct: 178 KAPGNLSVGAFVLPNNNPHDTLE 200
>gnl|CDD|240335 PTZ00259, PTZ00259, endonuclease G; Provisional.
Length = 434
Score = 187 bits (476), Expect = 2e-57
Identities = 89/230 (38%), Positives = 121/230 (52%), Gaps = 28/230 (12%)
Query: 4 GFPSLDSLRSFDDFVLSYDRRNRTAYWVFEHLTKE---NTAYSEAVNRSKSEFFEDDSIH 60
G PS ++LR ++ +V S + R WV E++ A + NR+ F+ D ++
Sbjct: 104 GLPSTENLRLYEGYVSSLNYERRIPNWVAEYIPYRGISVEAGEKKANRADCVFYADPTVP 163
Query: 61 EYFRGRNSDYKYSGYDRGHLAAAGNHKANQKHLDQTFVLSNISPQVGAGFNRDKWAELEK 120
E FR N DY SGY RGHLAAAG HKA+Q +D TF+LS N W LE
Sbjct: 164 EAFRAENKDYTGSGYSRGHLAAAGFHKASQTAMDDTFLLSANIVPQDLTNNAGDWLRLEN 223
Query: 121 HSRKLLKQY-PNVYVCTGPLYLP--------------------MKSPNG---KKYVNYEV 156
+RKL ++Y VYV +GPL++P SP KK V YEV
Sbjct: 224 LTRKLAREYEVGVYVVSGPLFVPRYMREKLRKWRLAEPSEIHKPDSPADKTPKKVVTYEV 283
Query: 157 IGDSNVAVPTHFFKIIVAENENGKLV-MENYVLPNAVISDSTPLTSFMVS 205
IGD+NVAVPTH FK+I+AE +G + +++PN IS PLT++ V
Sbjct: 284 IGDNNVAVPTHLFKVILAEKNDGPPHEVAAFLMPNEPISKEKPLTAYQVP 333
>gnl|CDD|214889 smart00892, Endonuclease_NS, DNA/RNA non-specific endonuclease. A
family of bacterial and eukaryotic endonucleases share
the following characteristics: they act on both DNA and
RNA, cleave double-stranded and single-stranded nucleic
acids and require a divalent ion such as magnesium for
their activity. An histidine has been shown to be
essential for the activity of the Serratia marcescens
nuclease. This residue is located in a conserved region
which also contains an aspartic acid residue that could
be implicated in the binding of the divalent ion.
Length = 198
Score = 175 bits (445), Expect = 2e-55
Identities = 80/195 (41%), Positives = 104/195 (53%), Gaps = 18/195 (9%)
Query: 14 FDDFVLSYDRRNRTAYWVFEHLTKENTAYSEAVNRSKSEFFEDD-SIHEYFRGRNSDYKY 72
+ + L YD R R WV HLT R + F D + F+ NSDY
Sbjct: 1 YKHYALCYDERRRLPLWVAYHLTGSTRQGKNT-GRKRPWFKPDGWHLPAIFQAVNSDYTG 59
Query: 73 SGYDRGHLAAAGNHKANQKHLDQTFVLSNISPQVGAGFNRDKWAELEKHSRKLLKQYPN- 131
SGYDRGHLA A +H +Q+ + TF L+NI PQ AGFN+ W LE + RKLL + +
Sbjct: 60 SGYDRGHLAPAADHGVSQEAMAATFYLTNIVPQT-AGFNQGNWNRLENYVRKLLAKNKDT 118
Query: 132 VYVCTGPLYLPMKSPNGKKYVNYEVIGDSNVAVPTHFFKIIVAENE-NGKLVMENYVLPN 190
VYV TGP+YLP N NVAVP+HF+K+I++E+ NG L + LPN
Sbjct: 119 VYVVTGPIYLPTLPDN-------------NVAVPSHFWKVILSEDGSNGGLAAIAFNLPN 165
Query: 191 AVISDSTPLTSFMVS 205
A I++ PL F V
Sbjct: 166 APINEDYPLCEFQVP 180
>gnl|CDD|216372 pfam01223, Endonuclease_NS, DNA/RNA non-specific endonuclease.
Length = 157
Score = 155 bits (393), Expect = 3e-48
Identities = 66/153 (43%), Positives = 83/153 (54%), Gaps = 12/153 (7%)
Query: 17 FVLSYDRRNRTAYWVFEHLTKENTAYSEAVNRSKSEFFEDDSIHEYFRGRNSDYKYSGYD 76
+ + YDRR R A WV HLT + A S R F ED I FR SDYK SG+D
Sbjct: 5 YSVCYDRRTRRALWVAHHLTGASLARSRGRRR-LDSFKEDPRIPAAFRATLSDYKGSGFD 63
Query: 77 RGHLAAAGNHKANQKHLDQTFVLSNISPQVGAGFNRDKWAELEKHSRKLLKQYPNVYVCT 136
RGHLA A A+ TF +N++PQ AGFNR WA LE + R L ++ +VYV T
Sbjct: 64 RGHLAPAAADFASTSAQKATFYYTNMAPQ-WAGFNRGNWAYLENYVRDLARKNRDVYVYT 122
Query: 137 GPLYLPMKSPNGKKYVNYEVIGDSNVAVPTHFF 169
GPL +P +G++ VAVPTHF+
Sbjct: 123 GPLGVP----------TLPTLGNNKVAVPTHFW 145
>gnl|CDD|224777 COG1864, NUC1, DNA/RNA endonuclease G, NUC1 [Nucleotide transport
and metabolism].
Length = 281
Score = 140 bits (355), Expect = 5e-41
Identities = 55/209 (26%), Positives = 93/209 (44%), Gaps = 21/209 (10%)
Query: 2 KYGFPSLDSLRSFDDFVLSYDRRNRTAYWVFEHLTKENTAYSEAVNRSKSEFFEDDSIHE 61
K G P+ L ++ F + Y+R + WV ++ + + + +FF D I E
Sbjct: 54 KDGLPN--YLLVYNHFSVVYNRSTKLPNWVAVNIDGSSLKKIK----RRDKFFPDTRIPE 107
Query: 62 YFRGRNSDYKYSGYDRGHLAAAGNHKANQKHLDQTFVLSNISPQVGAGFNRDKWAELEKH 121
+R SDYK SGYDRGH+ + + + TF ++N++PQ NR W ELE +
Sbjct: 108 KYRATLSDYKGSGYDRGHMVPPADGDFAIQANNDTFYMTNMTPQAAD-LNRKIWLELEDY 166
Query: 122 SRKLLKQYPNVYVCTGPLYLPMKSPNGKKYVNYEVIGDSNVAVPTHFFKIIVAENENGKL 181
R L ++Y +V + Y I + VAVP+ F+K++V ++G
Sbjct: 167 CRNLARKYGSVVIVFTGPYFRKDDT---------FIEKNKVAVPSEFWKVVVTLKKDGND 217
Query: 182 VMEN-----YVLPNAVISDSTPLTSFMVS 205
+ +PN + L ++ V
Sbjct: 218 SAAYLRVQAFYIPNLPGFRNGALKTYQVP 246
>gnl|CDD|184758 PRK14596, PRK14596, peptide deformylase; Provisional.
Length = 199
Score = 30.2 bits (68), Expect = 0.70
Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 78 GHLAAAGNHKANQKHLDQTFVLSNISPQVGAGF---NRDKWAELEKHSRKLLKQ 128
G+LA H+ + HLD + F +R + AE+++ ++ LK+
Sbjct: 140 GYLARVFQHEID--HLDGILFFDRLPKAKREAFLEAHRRELAEMQRQAKAYLKE 191
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.319 0.135 0.402
Gapped
Lambda K H
0.267 0.0682 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,311,889
Number of extensions: 1038652
Number of successful extensions: 909
Number of sequences better than 10.0: 1
Number of HSP's gapped: 887
Number of HSP's successfully gapped: 14
Length of query: 222
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 129
Effective length of database: 6,812,680
Effective search space: 878835720
Effective search space used: 878835720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (25.8 bits)